Recent studies have discovered that LPS-treated Sprague-Dawley rats induced a reduction (phase I), followed by an augmentation (phase II), and decrease again (phase III) in the power density of the vasomotor component (0-0.8 Hz) in systemic arterial pressure (SAP). It was reported that the vasomotor components were related to the brain stem, even closely related to the rostral ventrolateral medulla (RVLM). But the molecular mechanism involved in the death progression of rat brain stem is mostly unknown. We used suppression subtractive hybridization (SSH) and library construction to find differentially expressed genes between phase I and phase II of LPS-treated RVLM. At present, we have found some genes that are differentially expressed between phase I and phase II of LPS-treated RVLM. Some genes are up-regulation expression and others are down-regulation expression. Thus, these genes may be involved in the molecular mechanism of the death progression in the rat brain stem.

Malignant mesothelioma (MM) is an aggressive tumour, which is highly associated with previous asbestos exposure and is resistant to most conventional anticancer therapies. Previous studies have used a mouse model of to 01 p effective approaches to induction of anti-tumour immunity using modification of tumour cells by the introduction of genetic constructs expressing genes such as that for B7-1 so that tumour growth can be inhibited in vivo. Transfectant clones, AC29 B7-7 and AC29 B7-6, which showed equal levels of expression of B7-1 but were markedly different in tumorigenicity were assessed using suppression subtractive hybridization (SSH) in order to isolate transcripts which may have been differentially expressed in the two clones. SSH allowed isolation of a number of cDNAs which were apparently differentially expressed in the cell lines. These required characterisation in order to determine their possible relevance to tumorigenicity. Two cDNAs designated as 7-7-76 and 7-7-43 had been isolated previously and the aim of this project was to characterise these cDNAs by sequencing, searching for their homology relationships and investigating gene expression profiles. Preliminary searches revealed that clone 7-7-43 had homology to cyclin-dependent kinase regulatory subunit 1 which plays a role in the cell cycle. On the other hand, clone 77-76 showed only homology to an EST of hypertension related protein and therefore, further investigation was required to obtain the identity of clone 7-7-76. The first part of this project was to in investigate and evaluate gene expression on clone 7-7-43, using both relative RT-PCR and Northern blotting.' In the second part of this project, a more intense study of clone 7-7-76 was conducted. Clone 7-7-76 was investigated for its homology relationships and its gene expression profile. / Results obtained from relative RT-PCR suggested no difference in the expression of the either eDNA clone (7-7-43 and 7-7-76) between the MM clones AC29 B7-6 and AC29 B7-7, the cells used to derive these clones by SSH. Therefore, it was concluded that neither clone 7-7-43 nor 7-7-76 was differentially expressed in MM cells of differing immuno enicit RACE was employed in order to derive a longer sequence of clone 7-7-76 and the newly derived sequence of 7-7-76 was again used to search for homologies using a wider range of sequences for human and other species. These investigations on clone 7-7-76 showed it to correspond to the sequence of human mitofusin 2 which is involved in determining mitochondrial morphology The results determined in this project suggest that clones 7-7-43 and 7-7-76 are not differentially expressed in the range of MM cell lines tested. The data have however highlighted the potential of the SSH technique to easily derive cDNA clones worthy of investigation, but underline the possibility of false positive clones being isolated. The need for an efficient, accurate screening procedure such as real-time PCR is acknowledged.

Anxiety disorders are one of the most prevalent mental disorders in the world. While normal anxiety serves as an important protective mechanism, pathological anxiety characteristic of an anxiety disorder is both maladaptive and disruptive. The majority of studies have focused on the neurotransmitter systems associated with the actions of known anxiety drugs. This focus may likely limit the exploration of mechanisms underlying anxiety disorders. This project aims to examine changes in gene expression that may underlie higher or lower levels of inherent anxiety. Using a well-established behavior test for anxiety, the elevated plus maze, we identified male Wistar rats exhibiting inherently high- or low-anxiety levels. Brain regions known to mediate anxiety, the amygdala, hippocampus and nucleus accumbens, were dissected and total mRNA isolated. The mRNA was converted to cDNA via reverse transcription-polymerase chain reaction (RT-PCR). Then, the cDNA was used in suppression subtractive hybridization, a technique used to compare two complete populations of cDNAs and identify cDNAs that are upregulated in one population in relation to the other. In this project suppression subtractive hybridization was used to compare high- and low-anxiety cDNA populations. The upregulated cDNAs were amplified in a PCR reaction that enables rare transcripts to be identified. The PCR products from the suppression subtractive hybridization were cloned and used to create two cDNA libraries for high- and low-anxiety related genes. These clones were sequenced to show over 1000 genes upregulated in high- and low-anxiety. The gene list was then subjected to bioinformatic analysis to identify one candidate to be studied in further detail. <p>The prion protein was identified as a potential candidate. Examination of the literature sparked an interest in studying other prion-like proteins, more specifically the cytoplasmic polyadenylation element binding protein (CPEB). The CPEB protein is a potent regulator of mRNA translation in both mature oocytes and the adult brain. While unphosphorylated the CPEB protein keeps specific mRNAs dormant in the cytoplasm. In its phosphorylated form CPEB catalyzes polyadenylation of the mRNA, leading to protein synthesis. p*PCR was used to show the presence of CPEB mRNA transcripts in the rat hippocampus. CPEB protein expression was examined in the brain samples isolated from control, high- and low-anxiety rats. It was found that CPEB was significantly upregulated in high- and low-anxiety rats compared to control. The protein expression of an upstream kinase, Aurora A kinase, and a downstream target, Calcium/Calmodulin Dependent Kinase II (CaMKII), was also investigated. The results from Aurora A kinase were inconclusive. CaMKII, on the other hand, was significantly upregulated in high-anxiety over both control and low-anxiety. These results suggest that CPEB may catalyze increased translation of mRNAs in high-anxiety while acting as a repressor of those same mRNAs in low-anxiety. <p>Recent studies have suggested that CPEB protein plays an important role in synaptic plasticity. The regulation of synaptic plasticity, and its impact on learning and memory, is believed to be a key mechanism behind the maintenance of anxiety disorders. Therefore the results of this study suggest a new molecular mechanism in the development of anxiety disorders.

Anxiety disorders are one of the most prevalent mental disorders in the world. While normal anxiety serves as an important protective mechanism, pathological anxiety characteristic of an anxiety disorder is both maladaptive and disruptive. The majority of studies have focused on the neurotransmitter systems associated with the actions of known anxiety drugs. This focus may likely limit the exploration of mechanisms underlying anxiety disorders. This project aims to examine changes in gene expression that may underlie higher or lower levels of inherent anxiety. Using a well-established behavior test for anxiety, the elevated plus maze, we identified male Wistar rats exhibiting inherently high- or low-anxiety levels. Brain regions known to mediate anxiety, the amygdala, hippocampus and nucleus accumbens, were dissected and total mRNA isolated. The mRNA was converted to cDNA via reverse transcription-polymerase chain reaction (RT-PCR). Then, the cDNA was used in suppression subtractive hybridization, a technique used to compare two complete populations of cDNAs and identify cDNAs that are upregulated in one population in relation to the other. In this project suppression subtractive hybridization was used to compare high- and low-anxiety cDNA populations. The upregulated cDNAs were amplified in a PCR reaction that enables rare transcripts to be identified. The PCR products from the suppression subtractive hybridization were cloned and used to create two cDNA libraries for high- and low-anxiety related genes. These clones were sequenced to show over 1000 genes upregulated in high- and low-anxiety. The gene list was then subjected to bioinformatic analysis to identify one candidate to be studied in further detail. <p>The prion protein was identified as a potential candidate. Examination of the literature sparked an interest in studying other prion-like proteins, more specifically the cytoplasmic polyadenylation element binding protein (CPEB). The CPEB protein is a potent regulator of mRNA translation in both mature oocytes and the adult brain. While unphosphorylated the CPEB protein keeps specific mRNAs dormant in the cytoplasm. In its phosphorylated form CPEB catalyzes polyadenylation of the mRNA, leading to protein synthesis. p*PCR was used to show the presence of CPEB mRNA transcripts in the rat hippocampus. CPEB protein expression was examined in the brain samples isolated from control, high- and low-anxiety rats. It was found that CPEB was significantly upregulated in high- and low-anxiety rats compared to control. The protein expression of an upstream kinase, Aurora A kinase, and a downstream target, Calcium/Calmodulin Dependent Kinase II (CaMKII), was also investigated. The results from Aurora A kinase were inconclusive. CaMKII, on the other hand, was significantly upregulated in high-anxiety over both control and low-anxiety. These results suggest that CPEB may catalyze increased translation of mRNAs in high-anxiety while acting as a repressor of those same mRNAs in low-anxiety. <p>Recent studies have suggested that CPEB protein plays an important role in synaptic plasticity. The regulation of synaptic plasticity, and its impact on learning and memory, is believed to be a key mechanism behind the maintenance of anxiety disorders. Therefore the results of this study suggest a new molecular mechanism in the development of anxiety disorders.

Paracoccidioides brasiliensis, um fungo termodimórfico, é o agente causador da paracoccidioidomicose (PCM), a micose sistêmica prevalente da América Latina. A patogenicidade aparenta estar intimamente relacionada com a transição dimórfica da forma de micélio para a de levedura, que é induzida pela mudança da temperatura do ambiente pela temperatura do hospedeiro mamífero. Há poucas informações disponíveis sobre genes de P. brasiliensis que são necessários durante a fase patogênica. Nós, então, realizamos as técnicas de SSH (“Suppression Subtraction Hybridization") e de “Macroarray" com o objetivo de identificar genes que sejam preferencialmente expressos na fase leveduriforme do isolado Pb18. Genes identificados em ambos os procedimentos estão mais expressos na fase leveduriforme e estão envolvidos em metabolismo básico, transdução de sinal, crescimento e morfogênese e metabolismo do enxofre. Para testar se as mudanças observadas na expressão gênica refletem as diferenças entre as condições de crescimento usadas para obter as duas formas morfológicas preferivelmente às diferenças intrínsecas dos tipos celulares, nós realizamos experimentos com RT-PCR em tempo real utilizando preparações de RNA derivadas de ambas as fases, micélio e levedura, crescidas a 26°C e 37°C nos meios de cultura completos (YPD e Sabouraud) e meio mínimo. Vinte genes, incluindo AGS1 ( -1,3-glucan synthase) e TSA1 (thiol-specific antioxidant), foram mostrados como mais expressos na levedura patogênica em relação ao micélio. Embora a expressão de RNA mensageiro foi bastante diferente em relação aos meios completos e meio mínimo, mostramos uma tendência geral para que esses genes serem mais expressos nas células leveduriformes patogênicas de P.x brasiliensis. Além disso, mostramos a complementação dos genes METR e SCONC de P. brasiliensis e uma cepa com estes genes deletados de Aspergillus nidulans, sugerindo uma possível homologia entre eles. Mostramos também a análise de genes da via do metabolismo do enxofre foram mais expressos na levedura patogênica de P. brasiliensis em relação ao micélio saprofítico. / Paracoccidioides brasiliensis, a thermodimorphic fungus, is the causative agent of paracoccidioidomycosis (PCM), a prevalent systemic mycosis in Latin America. Pathogenicity appears to be intimately related to the dimorphic transition from the hyphal to the yeast form, which is induced by a shift from environmental temperature to the temperature of the mammalian host. Little information is available on the P. brasiliensis genes necessary during the pathogenic phase. We have therefore undertaken Suppression Subtraction Hybridization (SSH) and macroarray analyses with the aim of identifying genes that are preferentially expressed in the yeast phase. Genes identified by both procedures as being more highly expressed in the yeast phase are involved in basic metabolism, signal transduction, growth and morphogenesis, and sulfur metabolism. In order to test whether the observed changes in gene expression reflect the differences between the growth conditions used to obtain the two morphological forms rather than differences intrinsic to the cell types, we performed real-time RT-PCR experiments using RNA derived from both yeast cells and mycelia that had been cultured at 37 and 26°C in either complete medium (YPD or Sabouraud) or minimal medium. Twenty genes, including AGS1 ( 1,3-glucan synthase) and TSA1 (thiol-specific antioxidant), were shown to be more highly expressed in the yeast cells than in the hyphae. Although their levels of expression could be different in rich and minimal media, there was a general tendency for these genes to be more highly expressed in the yeast cells. Moreover, complementation of P. brasiliensis METR and SCONC genes in strains of Aspergillus nidulans with these genes deleted suggested a possible homology between them. We show the analyses of genes involved in the xii sulphur metabolism pathway and these genes were more expressed in the pathogenic yeast than saprophytic mycelia of P. brasiliensis.

Paracoccidioides brasiliensis, um fungo termodimórfico, é o agente causador da paracoccidioidomicose (PCM), a micose sistêmica prevalente da América Latina. A patogenicidade aparenta estar intimamente relacionada com a transição dimórfica da forma de micélio para a de levedura, que é induzida pela mudança da temperatura do ambiente pela temperatura do hospedeiro mamífero. Há poucas informações disponíveis sobre genes de P. brasiliensis que são necessários durante a fase patogênica. Nós, então, realizamos as técnicas de SSH (“Suppression Subtraction Hybridization”) e de “Macroarray” com o objetivo de identificar genes que sejam preferencialmente expressos na fase leveduriforme do isolado Pb18. Genes identificados em ambos os procedimentos estão mais expressos na fase leveduriforme e estão envolvidos em metabolismo básico, transdução de sinal, crescimento e morfogênese e metabolismo do enxofre. Para testar se as mudanças observadas na expressão gênica refletem as diferenças entre as condições de crescimento usadas para obter as duas formas morfológicas preferivelmente às diferenças intrínsecas dos tipos celulares, nós realizamos experimentos com RT-PCR em tempo real utilizando preparações de RNA derivadas de ambas as fases, micélio e levedura, crescidas a 26°C e 37°C nos meios de cultura completos (YPD e Sabouraud) e meio mínimo. Vinte genes, incluindo AGS1 ( -1,3-glucan synthase) e TSA1 (thiol-specific antioxidant), foram mostrados como mais expressos na levedura patogênica em relação ao micélio. Embora a expressão de RNA mensageiro foi bastante diferente em relação aos meios completos e meio mínimo, mostramos uma tendência geral para que esses genes serem mais expressos nas células leveduriformes patogênicas de P.x brasiliensis. Além disso, mostramos a complementação dos genes METR e SCONC de P. brasiliensis e uma cepa com estes genes deletados de Aspergillus nidulans, sugerindo uma possível homologia entre eles. Mostramos também a análise de genes da via do metabolismo do enxofre foram mais expressos na levedura patogênica de P. brasiliensis em relação ao micélio saprofítico. / Paracoccidioides brasiliensis, a thermodimorphic fungus, is the causative agent of paracoccidioidomycosis (PCM), a prevalent systemic mycosis in Latin America. Pathogenicity appears to be intimately related to the dimorphic transition from the hyphal to the yeast form, which is induced by a shift from environmental temperature to the temperature of the mammalian host. Little information is available on the P. brasiliensis genes necessary during the pathogenic phase. We have therefore undertaken Suppression Subtraction Hybridization (SSH) and macroarray analyses with the aim of identifying genes that are preferentially expressed in the yeast phase. Genes identified by both procedures as being more highly expressed in the yeast phase are involved in basic metabolism, signal transduction, growth and morphogenesis, and sulfur metabolism. In order to test whether the observed changes in gene expression reflect the differences between the growth conditions used to obtain the two morphological forms rather than differences intrinsic to the cell types, we performed real-time RT-PCR experiments using RNA derived from both yeast cells and mycelia that had been cultured at 37 and 26°C in either complete medium (YPD or Sabouraud) or minimal medium. Twenty genes, including AGS1 ( 1,3-glucan synthase) and TSA1 (thiol-specific antioxidant), were shown to be more highly expressed in the yeast cells than in the hyphae. Although their levels of expression could be different in rich and minimal media, there was a general tendency for these genes to be more highly expressed in the yeast cells. Moreover, complementation of P. brasiliensis METR and SCONC genes in strains of Aspergillus nidulans with these genes deleted suggested a possible homology between them. We show the analyses of genes involved in the xii sulphur metabolism pathway and these genes were more expressed in the pathogenic yeast than saprophytic mycelia of P. brasiliensis.

The objective of this study was to identify genes that are differentially regulated during diapause when compared with nondiapausing pupae in Sarcophaga crassipalpis. The results of a Suppression Subtractive Hybridization procedure was used to indentify genes that are differentially regulated in both diapause and nondiapausing states while suppressing genes that are common to both states. Randomly picked colonies from both subtractive libraries were isolated and the inserts sequenced. The sequences were analyzed using the bioinformatics tools NCBI, BlastX, Clustal W, etc. Out of 384 clones, 59 genes were found to be upregulated during diapause and 37 genes were found to be upregulated during a nondiapause pupal stage, no genes were found to be expressed commonly in both the diapause and nondiapause constructed libraries.

Yellow rust disease is one of the most important problems in wheat production. It causes substantial yield losses throughout the world. There are resistant and susceptible wheat varieties to various yellow rust pathotypes. In this thesis genes that are induced in wheat, in virulence and avirulence conditions upon yellow rust inoculations were investigated. Consequently, it was aimed to identify genes that may be playing critical roles in the disease resistance mechanism. The strategy was to construct subtracted cDNA libraries from resistant and susceptible plants and analyse the sequences obtained from these libraries. The subtraction approach in this study differs from the common subtraction designs implicated in plant-pathogen interactions / instead of comparing a compatible or an incompatible interaction with a control, one of the subtractions in this study is done taking a compatible interaction as the tester and an incompatible one as the driver, and the second subtraction, vice versa. Therefore, it was intended to compare the transcriptomes from compatible and incompatible plant-pathogen interactions directly. Suppression Subtractive Hybridization method was used to construct subtracted cDNA libraries. Two subtractions were performed / SSH1 (D-R), taking a compatible interaction as the tester sample and an incompatible one as the driver sample, and SSH2 (R-D), taking an incompatible interaction as the tester sample and a compatible one as the driver. In the end, two subtracted cDNA libraries, SSH1 (D-R) library (1536 clones) and SSH2 (R-D) library (1152 clones) were obtained and the libraries were sequenced. Sequence results were subjected to BlastN and BlastX analysis. We looked for a group of genes that were frequently emphasized in plant disease related studies when we searched within the Blast N homology results of the two libraries. We found out that 19 such genes are present in our libraries. We discussed supposed induction of these genes in the interactions investigated in our study. The fact that these genes were found to be present in our libraries enhances the reliability of our results suggesting that the gene sequences we found indeed belong to genes differentially expressed in the respective comparisons investigated in our study. As such, it also implies that other sequences that were found similar to genes of known functions may represent candidate genes as subjects of further studies investigating wheat-yellow rust interactions.

This is the first research by using suppression subtractive hybridization (SSH) to analysis the gene expression in marine macroalga Ulva fasciata Delile against excess copper toxicity, and it gives us a comprehensive understanding of the tolerant mechanism while macroalgae face to the excess copper. Suppression subtractive hybridization was used to identify genes differentially expressed following exposure to 50 £gM CuSO4 for 6- 12h in a marine macroalga Ulva fasciata Delile. In this work, 69 genes were identified, of which 55 were up-regulated and 14 were down-regulated. According to the database of Gene Ontology (GO), these genes were classified into 10 categories as follows: 1. Transcription; 2. Translation, ribosomal structure and biogenesis; 3. Posttranslational modification, protein turnover, chaperones; 4. Photosynthesis; 5. Cell redox homeostasis; 6. Stress; 7. Metabolism; 8. Energy production and conversion; 9. Transport; 10. Function unknown. According to the results, we suggest that the responses of U. fasciata against excess copper toxicity are mainly through increase of the energy production for providing sufficient energy to many metabolic pathways, and control of the Fe homeostasis and redox form of thiol groups for maintaining the cellular redox homeostasis, moreover, expression of photosynthetic genes for letting the photosynthesis work. In addition, to scavenge the ROS is by expression of stress-related genes, meanwhile, the proteins, DNA and lipids damaged by ROS (reactive oxygen species) and copper are repaired by expression of the other categorical genes. Over and above, the genes expressing in the metabolism category might maintain the amino acids homeostasis and increase the purine content, and subsequently increase the tolerant capacity of U. fasciata against excess copper toxicity. In addition, the concentrations of antioxidants and the activities and gene expression of antioxidant enzymes were determined in Ulva fasciata Delile by a 4-day exposure to 0, 5, 10, 20 and 50 £gM CuSO4. These results demonstrate that the maintenance of antioxidant homeostasis and the induction of activities of antioxidant enzymes via enhanced gene expression are used by U. fasciata to cope with the Cu-induced oxidative stress, but the defense capacity cannot sufficiently alleviate oxidative damage occurring under the condition of higher Cu concentrations. Moreover, according to the results from the expression of genes involved in the control of redox homeostasis and antioxidant defense was studied in macroalga Ulva fasciata Delile in response to CuSO4 (5 and 50 £gM) and ROS (H2O2 and O2£»-), we suggest that ROS involved in up-regulation of antioxidant defense-related genes and the expression of genes of antioxidant defense enzymes and UfMsrA (methionine sulfoxide reductase A) are associated with long-term adaptation of U. fasciata to Cu excess and transcription of redox- related genes and UfGr (glutathione reductase) is up-regulated for short-term acclimation. Promoters play a key role in regulating gene expression. Based on the analysis of cis-acting elements on UfMsr promoters, we suggested that the signal transduction pathway of copper stress in U. fasciata is related to that of other stresses and of defense-related plant hormones, however, Ca2+ and calmodulin might participate in it. To sum up, U. fasciata could resist oxidative damage caused by excessive copper through the regulation on the molecular level.

The pathogen Campylobacter fetus (CF) is classified into two subspecies, Campylobacter fetus subspecies fetus (CFF) and Campylobacter fetus subspecies venerealis (CFV). Even though CFF and CFV are genetically closely related, they exhibit differences in their host adaptation; CFF inhabits the gastrointestinal tract of both humans and several animal species, while classical CFV is specific to the bovine genital tract and is of particular concern with respect to international bovine trade regulation. Traditionally, differentiation between the two subspecies has been achieved using a limited number of biochemical tests but more rapid and definitive genetic methods of discrimination are desired. A recent study suggested that the presence of a genomic island only in CFV could discriminate between the two sub- species but this hypothesis could not be confirmed on a collection of isolates originating in Canada. To identify alternative gene targets that would support accurate subspecies discrimination, this study has applied several approaches including suppression subtractive hybridization and whole genome sequencing supplemented with optical mapping. A subtractive hybridization screen, using a well-characterized CFV isolate recovered during routine screening of bulls in an Artificial Insemination center in western Canada and that lacked much of the genomic island and a typical Canadian CFF isolate, yielded 50 clones; characterization of these clones by hybridization screening against selected CF isolates and by nucleotide sequence BLAST analysis identified three potentially CFV-specific clones that contained inserts originating from a second genomic island. Further screening using a larger CF sample set found that only Clone #35 was truly CFV-specific. Optical maps (NcoI digest) of the Canadian CFF and CFV isolates used for the subtractive hybridization showed that certain regions of these genomes were quite distinct from those of two reference strains. Whole genome sequencing of these two isolates identified two target genes (PICFV5_ORF548 and CFF_Feature #3) that appear to be selectively retained in the two subspecies. Screening of a collection of CF isolates by PCRs targeting these three loci (SSH_Clone #35, PICFV5_ORF548 and CFF_Feature #3) supported their use for subspecies discrimination. This work demonstrates the complex genomic diversity associated with these CF subtypes and the challenge posed by their discrimination using limited genetic loci.